Rafael A. Irizarry
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/affy |
| Branch: RELEASE_3_9 |
| Last Commit: 097ab4a |
| Last Changed Date: 2019-05-02 11:53:01 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:44:36 -0400 (Wed, 16 Oct 2019).
| Package 23/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| affy 1.62.0 Rafael A. Irizarry
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: affy |
| Version: 1.62.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:affy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings affy_1.62.0.tar.gz |
| StartedAt: 2019-10-16 00:25:05 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 00:28:15 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 189.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: affy.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:affy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings affy_1.62.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/affy.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affy/DESCRIPTION’ ... OK
* this is package ‘affy’ version ‘1.62.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘affy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘tkWidgets’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
‘stats:::C_loess_raw’ ‘stats:::C_lowesp’ ‘stats:::C_lowesw’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘bg.correct’
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
$.AffyBatch barplot.ProbeSet merge.AffyBatch pairs.AffyBatch
plot.ProbeSet
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function calls to a base package:
.C(stats:::C_loess_raw, ...)
.Fortran(stats:::C_lowesp, ...)
.Fortran(stats:::C_lowesw, ...)
Packages should not make .C/.Call/.External/.Fortran calls to a base
package. They are not part of the API, for use only by R itself and
subject to change without notice.
* checking R code for possible problems ... NOTE
AllButCelsForReadAffy: no visible global function definition for
‘fileBrowser’
AllButCelsForReadAffy: no visible global function definition for
‘hasSuffix’
expressoWidget: no visible global function definition for ‘tclVar’
expressoWidget : quit: no visible global function definition for
‘tkdestroy’
expressoWidget : end: no visible global function definition for
‘tclvalue’
expressoWidget: no visible global function definition for ‘tktoplevel’
expressoWidget: no visible global function definition for ‘tkdestroy’
expressoWidget: no visible global function definition for ‘tktitle<-’
expressoWidget: no visible global function definition for ‘tkpack’
expressoWidget: no visible global function definition for ‘tklabel’
expressoWidget: no visible global function definition for ‘tkframe’
expressoWidget: no visible global function definition for
‘dropdownList’
expressoWidget: no visible global function definition for ‘tclvalue’
expressoWidget: no visible global function definition for ‘tkgrid’
expressoWidget: no visible global function definition for
‘tkgrid.configure’
expressoWidget: no visible global function definition for ‘tkbutton’
expressoWidget: no visible global function definition for
‘tkwait.window’
Undefined global functions or variables:
dropdownList fileBrowser hasSuffix tclVar tclvalue tkbutton tkdestroy
tkframe tkgrid tkgrid.configure tklabel tkpack tktitle<- tktoplevel
tkwait.window
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
mas5 40.074 0.310 40.395
expresso 18.271 0.272 18.899
MAplot 15.528 0.985 16.838
AffyBatch-class 4.832 0.392 5.232
ProgressBarText-class 1.030 0.077 16.762
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/affy.Rcheck/00check.log’
for details.
affy.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL affy ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘affy’ ... ** using staged installation creating cache ./config.cache checking how to run the C preprocessor... cc -E checking for main in -lz... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes updating cache ./config.cache creating ./config.status creating src/Makevars ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/preprocessCore/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c chipbackground.c -o chipbackground.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/preprocessCore/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c getall_locations.c -o getall_locations.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/preprocessCore/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c mas5calls.c -o mas5calls.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/preprocessCore/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c rma2.c -o rma2.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/preprocessCore/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c rma_common.c -o rma_common.o clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-affy/00new/affy/libs ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (affy)
affy.Rcheck/affy-Ex.timings
| name | user | system | elapsed | |
| AffyBatch-class | 4.832 | 0.392 | 5.232 | |
| AffyRNAdeg | 2.706 | 0.193 | 2.900 | |
| MAplot | 15.528 | 0.985 | 16.838 | |
| ProbeSet-class | 0.511 | 0.035 | 0.585 | |
| ProgressBarText-class | 1.030 | 0.077 | 16.762 | |
| affy-options | 0.001 | 0.001 | 0.002 | |
| barplot.ProbeSet | 0.602 | 0.029 | 0.633 | |
| bgc | 2.329 | 0.299 | 2.656 | |
| cleancdfname | 0.009 | 0.002 | 0.011 | |
| expresso | 18.271 | 0.272 | 18.899 | |
| expressoWidget | 0.001 | 0.000 | 0.001 | |
| fit.li.wong | 0.291 | 0.019 | 0.310 | |
| generateExprSet-methods | 0.622 | 0.012 | 0.633 | |
| generateExprVal-methods | 0.540 | 0.015 | 0.555 | |
| generateExprVal.method.avgdiff | 0.446 | 0.062 | 0.510 | |
| list.celfiles | 0.000 | 0.001 | 0.001 | |
| maffy.subset | 0.022 | 0.001 | 0.023 | |
| mas5 | 40.074 | 0.310 | 40.395 | |
| mas5calls | 1.722 | 0.130 | 1.853 | |
| mva.pairs | 0.110 | 0.004 | 0.114 | |
| normalize-methods | 0.442 | 0.038 | 0.480 | |
| normalize.loess | 0.023 | 0.001 | 0.024 | |
| plot.ProbeSet | 0.015 | 0.004 | 0.019 | |
| plot.density | 0.937 | 0.143 | 1.080 | |
| plotLocation | 1.937 | 0.186 | 2.129 | |
| pmcorrect | 0.434 | 0.029 | 0.464 | |
| ppsetApply | 0.002 | 0.000 | 0.002 | |
| read.affybatch | 2.129 | 0.166 | 2.303 | |
| rma | 1.750 | 0.048 | 1.798 | |
| setAffyOptions | 0.000 | 0.001 | 0.001 | |
| xy2indices | 1.969 | 0.222 | 2.205 | |